NOTE: the best way to figure out what you need to work on is to do 'Ctrl+F' and search for your name. Hit 'enter' to find the next instance. - Thanks, Dr. B
----- this assumes I haven't misspelled your name!
NOTES for PyMol 1
- show them Alt + i + t for time stamp
- have them open and use UTBox
- how to force Firefox to download a file to a folder you specify
- don't need pics for Warmups
- their Word doc does not need to be typed verbatim from handout. They can copy and paste the procedure steps, but must add in comentary/analysis
TA TASKS- Joey
Lab notebook grading
MENTOR TASKS
Week of MLK
Lit Search and Bibliography assignment reviewing (see ReviewingLitSearchforMentorsGDocsSp14 in VDSStaff GDocs) - KAVYA, NICOLE
-- determine # of days late for each student using the Image file in the same folder that has the submission dates -- copies are in Dr. B's Pigeon Hole, write directly on the papers and indicate points off out of total points and then indicate # of points off for days late. DUE DATE: Monday during the day - so that Dr. B can hand them back in class on Tuesday
Comment on Lab Notebooks (see your assignments on the **LabNotebookCommentingforMentorsSp14** in VDSStaff GDocs) - ALL
-- After the students turn their lab notebooks in on Friday and Saturday, you can begin commenting.
---------(they turn them in on Saturday at the latest - but once a grading rubric is on there - you can start looking at it.)
-- for the 4-5 notebooks which you have been assigned, go through them and write comments directly in the notebook (blu ink preferred)
-- Also, as you go, please circle or underline items on the Lab Notebook Grading Rubric that would help Joey in grading. (e.g. missing analysis, materials not listed, no page numbers, etc.)
-- Joey will go back through and apply a score to each one. Then Dr. B will approve them. DUE DATE: Monday night/Tuesday during the day of PyMol1 week - so that Joey and I have time to look at them.
'Starter Questions' for the TEAM meetings - to help your students get to know you better
QUESTIONS FOR THE WHOLE GROUP
Favorite place on the Drag (or around the 40 acres but not on campus)?
Where are you from? What high school did you go to?
How is your adjustment to UT going?
Favorite/Least favorite [[#|classes this]] semester? Any particular classes you are concerned about?
What are your majors?
What are your career interests?
What do you think of VDS so far? Favorite aspects? Least favorite aspects?
Which do you prefer - wet lab or computer labs?
Do you have any concerns about the labs?
Do you have any questions regarding the concepts underlying the labs?
What do you hope to get out of this experience?
What are your research interests?
Since this is VDS, what is your favorite drug/molecule?
General points to cover (by the TEAM leaders):
- basic intro (major, year, etc.)
- overview of what they can expect from VDS (short- and long-term)
- how VDS has helped you and why it is beneficial for them to stick with it
- your research interests and experiences
- your career plans and what stage you are at now
- Why VDS is the best stream!
From the Mini-Research Write Up Page (wait until they have turned in their 1st Mini Research Write Up as PDF.)
--Create a Wikispaces page for each Disease (no student name on there)
Modify LabNotebook Reviewing assignments sheet in VDSStaff GDocs.
-- update roster - DONE JOEY
-- for each student in the spreadsheet - put in their Team name in a new column - DONE JOEY
-- assign each mentor to the students in their group -DONE Dr. B
Teaching Assistant's Stuff - Joey
Go over Lab Notebook Grading Rubric & Lab Notebook spreadsheet
Make Sign-In Sheet for Lab (for PAI 2.14 folder) - will probably be 2 sheets each week (in Gdocs, download, edit and re-upload)
ADMINISTRATIVE/OFFICE WORK
come up with a lab 'mission statement' - ALL
Please Print, Read and Sign the Mentor Contracts. Then return to Dr. B - ALL --- Mentor Contract on GDocs
update mentor schedules - DONE
update Class Schedule - GRACE
Take pictures of staff (group and individuals - upload to VDSStaff in GDocs, Upload to Wiki Mentors Sp14 page) - DONE
Generate a time sheet - PAID MENTORS
post Labnotebook Grading rubric to Wiki (upload PDF then in space.menu on lhs - make link to file) - ANITA
post Labnotebook vs LabReport to Wiki (upload PDF then in space.menu on lhs - make link to file) - VICKY
In 'Pigeon Holes' for lab notebooks
organize pigeon holes by moving VDS Alums to the other lab notebook stacks - TONY (DONE)
make new name plate sheets (out of manila folders) - KAVYA - (DONE)
organize binders (Student one and Mentor one) - DONE
Mentor Folder:
create and print new hourly sign-in sheet (don't need to do TA though) - see old one in GDocs either VDSStaff or /Mentors
make tabs for each mentor - see GDocs/Mentors/ Schedule sheet to get Mentor names (dont do TA because she does not do timesheets) -
get some extra blue sheets to include in folder
Student Folder:
remove old safety training (except for people still working in lab (e.g. mentors and researchers)
put new sign in sheet for students (get from the TA)
make picture roster of students and staff pics (get photo roster from Dr. B - but add in staff pictures)
make Mentor name tags with VDS logo on them (talk to Dr. B - may have to use Dr. B's printer? Might work on lab printer in manual feed mode) - DONE
TEAMS (on Piazza and Wikispaces) - NICOLE
create a TEAMS Sp14 page in Wikispaces
add link in the menu on the left hand side of Wikispaces
create TEAMS by of about 5-7 students (#of students/# of mentors) per Team by UTEID alphabetical
Make a Google Spreadsheet in GDocs/VDSclass/Misc that shows all of the Team, Mentor leaders, and team name
- embed this spreadsheet into the Wikispaces page (Grace needs to learn embedding too - so get her when Dr. B shows you this step)
Create the same TEAMS in Piazza
- Dr. B needs to make the Piazza page first
- add link to Wikispaces to Piazza (place on space.menu on left and on TEAMS Sp14 page)
ANNOUNCE TEAMS IN VDS 1st Class ???
Once TEAMS are made - edit the TEAMS SIgns Sp14.docx in the VDSStaff GDocs/Misc and let Dr. B know (he will use it in class) - NICOLE
WIKISPACES WORK
create Wikispaces pages for each student for Protein Labs (create new page Protein Labs Sp14) - ANITA
CATALOGING PURCHASING INTO EXCEL SPREADSHEET FROM FALL 13
-- place receipts in Dr. B's receipts pigeon hole
Lab Safety
create Lab Safety Sp14 page in Wikispaces with names of each students and table, link from left hand menu - PRIYA (done -Anita Thanks Anita <3 )
Practice Lab Safety Walk Throughs - TONY, ANITA, PRIYA (DONE)
Lab Safety Videos posted to Wikispaces and Generate Quizzes in Canvas based on Procko work - TONY, ANITA
LAB WORK
clean lab - ALL
clean out top loading -20degC freezer - remove old Biobricks stuff and create a new label for VDS on a metal rack. - PRIYA
organize and label -80degC freezer racks - DONE
unpacking supplies, labeling and storing them
Transformation of pGBR22 in DH5alpha AMP plates - PRIYA
Blue Juice for protein gels - PRIYA (Waiting on DTT)
Make some YopH
-- Tony Transformation, Expression, Sonication (DONE)
-- Nicole Purification (Ni-NTA), FPLC, Storage in Glycerol
walk through Buffer & Solutions -
First pipetting steps with Excel graphof Buffers & Solutions KAVYA, GRACE
200 ml 0.1 M Tris Base pH 7.5 – pH meter, acids (calibrate pH meter as part of this, test out new pH probes)- DONE
Kanamycin – syringe filter - SERENA
THIS WEEK:
walk through the Beer’s Law lab - PRIYA, KAVYA
walk through Titration lab - DONE
walk through virtual labs
Rinse the 'clean' collirollers in nanopure water, transfer to a clean bottle, label - then Autoclave (use autoclave tape) - SERENA
Autoclave Nanopure water, label, store in Cubby. Make 2 x 500ml. - this is for 1st Lab to make 30% EtOH - GRACE
Autoclave colirollers - SERENA
divide up colirrolers in to 6 rollers each in sterile tubes of (600 ul tubes) - make a full ~ 80 tube rack of these - SERENA & GRACE
ASSESSMENT
Pre and Post Surveys (SURE research surveys are online) - DONE
look up how to use and implement
Update Laptops and Desktops - TONY, KAVYA (DONE)
Clean off old icons from Desktops of Desktop & Laptop computers
Do Windows Updates on laptops
SOLUTIONS INSTRUCTIONS:
(also see the Solutions&Dilutions Spreadsheet on GDocs for help with calculations)
Make LB - 2Liters - and autoclave Make 5 M NaCl - 500 ml in water, sterile filter into a bottle, label, store at Room Temp
Make Kanamycin- stocks 50ug/ul store in -20degC, Make 30 tubes of 500 ul each. Sterile filter with syringe filterbefore aliquoting into tubes. Label. Store in -20degC
Make IPTG - 1 M IPTG stock to make. Make 30 tubes of this with 500 ul in each. Label. Store in -20degC
Make Lysozyme - 20 aliquots of 500 ul at 50 mg/ml in 1.7 ml tubes. Label. Store in -20degC
Make TCEP - make ~50 x 100ul aliquots of 500 mM aliquots medium size centrifuge tubes. Label, put in a box and Store at Room Temp in cubby.
Make PMSF - 30 x 500 ul aliquots of 10mM in Isopropanol 1.7 ml tubes. Label. store in -20degC
Make Imidazole - 1M stock make in beaker of 500 ml of water, then bottle top sterile filter it into a bottle, store at Room Temp
Lysis Buffer for Sonication (make 500 ml)
(see GDocs 'Solutions&Dilutions' in /Misc folder for calculations)
Tris 100 mM
NaCl 300 mM
Imidazole 30 mM
pH 8.0 w/ NaOH
label, store at 4degC
NEW Wash and Elution Buffers and Storage Buffer(see GDocs 'Solutions&Dilutions' in /Misc folder for calculations)
Wash Buffer
Tris 100 mM
NaCl 300 mM
Imidazole 30 mM
pH 8.0 w/ NaOH
Elution Buffer
Tris 100 mM
NaCl 300 mM
Imidazole 300 mM
pH 8.0 w/ NaOH
FPLC column buffer - tris Also 'storage' buffer
Tris 50 mM
NaCl 150 mM
pH 8.0 w/ NaOH
Then filter sterilize
Then degass**
6X SDS Page Buffer from 5 Prime Protocol
30 ml of glycerol – add first so that you can see the volume (viscous)
(In a separate tube) - 30 ml of Nanopure water
--- 1.635 g Tris powder
--- 3 g SDS poweder
--- 0.3 g Bromophenol blue
----2.3136 g DTT
Mix contents of second tube into tube with glycerol
Add some more Nanopure water to 50 ml total final volume
Mentor Info and Tasks:
Calendar for Staff Sp14
Use the MentorLabLog on GDocs/VDSstaff for as a Lab Notebook for Wet Lab tasksTeaching Points for Labs Sp14
-- also see folder in VDS Staff Google Docs account-- contains lab handout and teaching points sheets
MENTORS: ANITA, TONY, GRACE, KAVYA, NICOLE, PRIYA, SERENA, VICKY, MELISSA,
TA: JOEY
NOTE: the best way to figure out what you need to work on is to do 'Ctrl+F' and search for your name. Hit 'enter' to find the next instance. - Thanks, Dr. B
----- this assumes I haven't misspelled your name!
Packages: Open, figure out if it is VDS, show to Owais if there, Label appropriately, Place in proper storage, Give receipt to Dr. B and let him know it has arrived and is stored
Please fill out your weekly schedule here:
https://docs.google.com/spreadsheet/ccc?key=0AvGl3lMyhDsodDBwM3ZZQ3RpbVVMbVlpdDd1bFFXVkE&usp=sharing
NOTES for PyMol 1
- show them Alt + i + t for time stamp
- have them open and use UTBox
- how to force Firefox to download a file to a folder you specify
- don't need pics for Warmups
- their Word doc does not need to be typed verbatim from handout. They can copy and paste the procedure steps, but must add in comentary/analysis
TA TASKS- Joey
Lab notebook gradingMENTOR TASKS
Week of MLK
Lit Search and Bibliography assignment reviewing (see ReviewingLitSearchforMentorsGDocsSp14 in VDSStaff GDocs) - KAVYA, NICOLE
-- determine # of days late for each student using the Image file in the same folder that has the submission dates
-- copies are in Dr. B's Pigeon Hole, write directly on the papers and indicate points off out of total points and then indicate # of points off for days late.
DUE DATE: Monday during the day - so that Dr. B can hand them back in class on Tuesday
Comment on Lab Notebooks (see your assignments on the **LabNotebookCommentingforMentorsSp14** in VDSStaff GDocs) - ALL
-- After the students turn their lab notebooks in on Friday and Saturday, you can begin commenting.
---------(they turn them in on Saturday at the latest - but once a grading rubric is on there - you can start looking at it.)
-- for the 4-5 notebooks which you have been assigned, go through them and write comments directly in the notebook (blu ink preferred)
-- Also, as you go, please circle or underline items on the Lab Notebook Grading Rubric that would help Joey in grading. (e.g. missing analysis, materials not listed, no page numbers, etc.)
-- Joey will go back through and apply a score to each one. Then Dr. B will approve them.
DUE DATE: Monday night/Tuesday during the day of PyMol1 week - so that Joey and I have time to look at them.
'Starter Questions' for the TEAM meetings - to help your students get to know you better
QUESTIONS FOR THE WHOLE GROUP
General points to cover (by the TEAM leaders):
- basic intro (major, year, etc.)- overview of what they can expect from VDS (short- and long-term)
- how VDS has helped you and why it is beneficial for them to stick with it
- your research interests and experiences
- your career plans and what stage you are at now
- Why VDS is the best stream!
From the Mini-Research Write Up Page (wait until they have turned in their 1st Mini Research Write Up as PDF.)
--Create a Wikispaces page for each Disease (no student name on there)
Modify LabNotebook Reviewing assignments sheet in VDSStaff GDocs.
-- update roster - DONE JOEY
-- for each student in the spreadsheet - put in their Team name in a new column - DONE JOEY
-- assign each mentor to the students in their group -DONE Dr. B
Teaching Assistant's Stuff - Joey
Go over Lab Notebook Grading Rubric & Lab Notebook spreadsheetMake Sign-In Sheet for Lab (for PAI 2.14 folder) - will probably be 2 sheets each week (in Gdocs, download, edit and re-upload)
ADMINISTRATIVE/OFFICE WORK
come up with a lab 'mission statement' - ALLPlease Print, Read and Sign the Mentor Contracts. Then return to Dr. B - ALL
--- Mentor Contract on GDocs
update mentor schedules - DONE
update Class Schedule - GRACE
Take pictures of staff (group and individuals - upload to VDSStaff in GDocs, Upload to Wiki Mentors Sp14 page) - DONE
Generate a time sheet - PAID MENTORS
post Labnotebook Grading rubric to Wiki (upload PDF then in space.menu on lhs - make link to file) - ANITA
post Labnotebook vs LabReport to Wiki (upload PDF then in space.menu on lhs - make link to file) - VICKY
In 'Pigeon Holes' for lab notebooks
organize pigeon holes by moving VDS Alums to the other lab notebook stacks - TONY (DONE)make new name plate sheets (out of manila folders) - KAVYA - (DONE)
organize binders (Student one and Mentor one) - DONE
Mentor Folder:
- print new timesheet pay periods sheet (from UT webpage - Timesheet Pay Periods and Due Dates (see bottom of link)
- create and print new hourly sign-in sheet (don't need to do TA though) - see old one in GDocs either VDSStaff or /Mentors
- make tabs for each mentor - see GDocs/Mentors/ Schedule sheet to get Mentor names (dont do TA because she does not do timesheets) -
- get some extra blue sheets to include in folder
Student Folder:make Mentor name tags with VDS logo on them (talk to Dr. B - may have to use Dr. B's printer? Might work on lab printer in manual feed mode) - DONE
TEAMS (on Piazza and Wikispaces) - NICOLE
create a TEAMS Sp14 page in Wikispaces
add link in the menu on the left hand side of Wikispaces
create TEAMS by of about 5-7 students (#of students/# of mentors) per Team by UTEID alphabetical
Make a Google Spreadsheet in GDocs/VDSclass/Misc that shows all of the Team, Mentor leaders, and team name
- embed this spreadsheet into the Wikispaces page (Grace needs to learn embedding too - so get her when Dr. B shows you this step)
Create the same TEAMS in Piazza
- Dr. B needs to make the Piazza page first
- add link to Wikispaces to Piazza (place on space.menu on left and on TEAMS Sp14 page)
ANNOUNCE TEAMS IN VDS 1st Class ???
Once TEAMS are made - edit the TEAMS SIgns Sp14.docx in the VDSStaff GDocs/Misc and let Dr. B know (he will use it in class) - NICOLE
WIKISPACES WORK
CATALOGING PURCHASING INTO EXCEL SPREADSHEET FROM FALL 13
-- place receipts in Dr. B's receipts pigeon hole
Lab Safety
create Lab Safety Sp14 page in Wikispaces with names of each students and table, link from left hand menu - PRIYA (done -Anita Thanks Anita <3 )Practice Lab Safety Walk Throughs - TONY, ANITA, PRIYA (DONE)
Lab Safety Videos posted to Wikispaces and Generate Quizzes in Canvas based on Procko work - TONY, ANITA
LAB WORK
clean lab - ALLclean out top loading -20degC freezer - remove old Biobricks stuff and create a new label for VDS on a metal rack. - PRIYA
organize and label -80degC freezer racks - DONE
unpacking supplies, labeling and storing them
Transformation of pGBR22 in DH5alpha AMP plates - PRIYA
Blue Juice for protein gels - PRIYA (Waiting on DTT)
Make some YopH
-- Tony Transformation, Expression, Sonication (DONE)
-- Nicole Purification (Ni-NTA), FPLC, Storage in Glycerol
walk through Buffer & Solutions -
THIS WEEK:
walk through the Beer’s Law lab - PRIYA, KAVYA
walk through Titration lab - DONE
walk through virtual labs
Rinse the 'clean' collirollers in nanopure water, transfer to a clean bottle, label - then Autoclave (use autoclave tape) - SERENA
Autoclave Nanopure water, label, store in Cubby. Make 2 x 500ml. - this is for 1st Lab to make 30% EtOH - GRACE
Autoclave colirollers - SERENA
divide up colirrolers in to 6 rollers each in sterile tubes of (600 ul tubes) - make a full ~ 80 tube rack of these - SERENA & GRACE
ASSESSMENT
Pre and Post Surveys (SURE research surveys are online) - DONE
Update Laptops and Desktops - TONY, KAVYA (DONE)
SOLUTIONS INSTRUCTIONS:
(also see the Solutions&Dilutions Spreadsheet on GDocs for help with calculations)Make LB - 2Liters - and autoclave
Make 5 M NaCl - 500 ml in water, sterile filter into a bottle, label, store at Room Temp
Make Kanamycin- stocks 50ug/ul store in -20degC, Make 30 tubes of 500 ul each. Sterile filter with syringe filterbefore aliquoting into tubes. Label. Store in -20degC
Make IPTG - 1 M IPTG stock to make. Make 30 tubes of this with 500 ul in each. Label. Store in -20degC
Make Lysozyme - 20 aliquots of 500 ul at 50 mg/ml in 1.7 ml tubes. Label. Store in -20degC
Make TCEP - make ~50 x 100ul aliquots of 500 mM aliquots medium size centrifuge tubes. Label, put in a box and Store at Room Temp in cubby.
Make PMSF - 30 x 500 ul aliquots of 10mM in Isopropanol 1.7 ml tubes. Label. store in -20degC
Make Imidazole - 1M stock make in beaker of 500 ml of water, then bottle top sterile filter it into a bottle, store at Room Temp
Lysis Buffer for Sonication (make 500 ml)
(see GDocs 'Solutions&Dilutions' in /Misc folder for calculations)Tris 100 mM
NaCl 300 mM
Imidazole 30 mM
pH 8.0 w/ NaOH
label, store at 4degC
NEW Wash and Elution Buffers and Storage Buffer(see GDocs 'Solutions&Dilutions' in /Misc folder for calculations)
Wash Buffer
Tris 100 mM
NaCl 300 mM
Imidazole 30 mM
pH 8.0 w/ NaOH
Elution Buffer
Tris 100 mM
NaCl 300 mM
Imidazole 300 mM
pH 8.0 w/ NaOH
FPLC column buffer - tris Also 'storage' buffer
Tris 50 mM
NaCl 150 mM
pH 8.0 w/ NaOH
Then filter sterilize
Then degass**
6X SDS Page Buffer from 5 Prime Protocol
30 ml of glycerol – add first so that you can see the volume (viscous)(In a separate tube) - 30 ml of Nanopure water
--- 1.635 g Tris powder
--- 3 g SDS poweder
--- 0.3 g Bromophenol blue
----2.3136 g DTT
Mix contents of second tube into tube with glycerol
Add some more Nanopure water to 50 ml total final volume
010914 - see revised Beginning of Semester Q's Ver2
Please fill out the
VDSstaffBeginningofSemesterQ's
https://docs.google.com/spreadsheet/viewform?formkey=dDNjTjlhdTlaM1BZWE9TNEVEdnlIeHc6MA#gid=0
Printer Installation
- Login as Mentor, Start Menu,
- Devices And printers
- Add New Printer
- Add "local" printer
- Create New Port --> standard TCP pathway
- Enter IP 128.82.195.186
- Printer Name Lexmark C543
- Add Printer (if can't find printer do Window Update)
For installation of a different Printer (such as Dell) change the IP address and Printer NamePrinter Name: Lexmark C543 IP: 128.83.195.186
Printer Name: Dell IP: 129.116.152.49
MentorsSp13 (last year's mentors page)